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Yorodumi- PDB-4lub: X-ray structure of prephenate dehydratase from Streptococcus mutans -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lub | ||||||
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Title | X-ray structure of prephenate dehydratase from Streptococcus mutans | ||||||
Components | Putative prephenate dehydratase | ||||||
Keywords | LYASE / dehydratase / dehydration | ||||||
Function / homology | Function and homology information prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Shin, H.H. / Ku, H.K. / Song, J.S. / Choi, S. / Son, S.Y. | ||||||
Citation | Journal: TO BE PUBLISHED Title: X-ray structure of prephenate dehydratase from Streptococcus mutans Authors: Shin, H.H. / Ku, H.K. / Song, J.S. / Choi, S. / Son, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lub.cif.gz | 171.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lub.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/4lub ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4lub | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31179.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: pheA, SMU_786 / Plasmid: PET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DUV6, prephenate dehydratase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 15% polyethylene glycol 8000, 100mM magnesium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399 Å |
Detector | Type: Photonic science VHR CCD / Detector: CCD / Date: Dec 6, 2009 |
Radiation | Monochromator: DMM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 |
Reflection | Resolution: 2.097→34.9 Å / Num. all: 25696 / Num. obs: 25692 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 20.97 Å2 / Rmerge(I) obs: 0.0871 / Net I/σ(I): 14.86 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.0871 / Mean I/σ(I) obs: 14.86 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→34.877 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→34.877 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.2841 Å / Origin y: 13.5826 Å / Origin z: 18.2263 Å
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Refinement TLS group | Selection details: ALL |